Package: puremoe 1.1.0
Jason Timm
puremoe: Integrated Retrieval and Analysis of 'PubMed', 'NIH', and 'NLM' Literature Data
Retrieve and analyze biomedical literature from 'PubMed' and the wider 'NIH'/'NLM' data stack through a single, PMID-centered interface. A PubMed search resolves to a set of PMIDs, which can be used to retrieve article metadata and abstracts, author affiliations, 'iCite' citation data and links, 'PubTator3' entity and relation annotations, and open-access full text from 'PMC'. A local analysis layer operates on the retrieved tables, supporting corpus expansion through citation links, citation network construction, sentence-level entity co-occurrence, inspection of relation evidence, and 'MeSH' descriptor keyness.
Authors:
puremoe_1.1.0.tar.gz
puremoe_1.1.0.zip(r-4.7)puremoe_1.1.0.zip(r-4.6)puremoe_1.1.0.zip(r-4.5)
puremoe_1.1.0.tgz(r-4.6-any)puremoe_1.1.0.tgz(r-4.5-any)
puremoe_1.1.0.tar.gz(r-4.7-any)puremoe_1.1.0.tar.gz(r-4.6-any)
puremoe_1.1.0.tgz(r-4.6-emscripten)
manual.pdf |manual.html✨
DESCRIPTION |NEWS
card.svg |card.png
puremoe/json (API)
| # Install 'puremoe' in R: |
| install.packages('puremoe', repos = c('https://jaytimm.r-universe.dev', 'https://cloud.r-project.org')) |
Bug tracker:https://github.com/jaytimm/puremoe/issues
Pkgdown/docs site:https://jaytimm.github.io
- data_mesh_frequencies - MeSH Descriptor Frequencies Across PubMed
Last updated from:b6f40cb95d. Checks:9 OK. Indexed: yes.
| Target | Result | Time | Files | Syslog |
|---|---|---|---|---|
| linux-devel-x86_64 | OK | 147 | ||
| source / vignettes | OK | 207 | ||
| linux-release-x86_64 | OK | 157 | ||
| macos-release-arm64 | OK | 137 | ||
| macos-oldrel-arm64 | OK | 80 | ||
| windows-devel | OK | 117 | ||
| windows-release | OK | 120 | ||
| windows-oldrel | OK | 117 | ||
| wasm-release | OK | 144 |
Exports:citation_networkcitation_snowballdata_mesh_thesaurusdata_mesh_treesendpoint_infoget_recordsmesh_keynesspmid_to_ftppmid_to_pmcpubtator_contextpubtator_cooccurrencepubtator_networksearch_pubmed
Dependencies:askpassclicpp11curldata.tablegenericsgluehttrjsonlitelatticelifecyclelubridatemagrittrMatrixmimeopensslpbapplypillarpkgconfigR6rappdirsrentrezrlangrvestselectrslamstringistringrsystextpresstextshapetibbletimechangeutf8vctrsXMLxml2
Readme and manuals
Help Manual
| Help page | Topics |
|---|---|
| Build a Citation Network from an iCite Corpus | citation_network |
| Expand a PMID Corpus via One-Hop iCite Citation Snowballing | citation_snowball |
| MeSH Descriptor Frequencies Across PubMed | data_mesh_frequencies |
| Download and Combine 'MeSH' and Supplemental Thesauruses | data_mesh_thesaurus |
| Download and Load 'MeSH' Trees Data | data_mesh_trees |
| Get Information About Available Endpoints | endpoint_info |
| Retrieve Data from 'NLM'/'PubMed' databases Based on PMIDs | get_records |
| MeSH Descriptor Keyness for a Retrieved Corpus | mesh_keyness |
| Convert PubMed IDs (PMIDs) to PMC IDs and Full-Text URLs | pmid_to_ftp |
| Convert PubMed IDs (PMIDs) to PMC IDs | pmid_to_pmc |
| Add Sentence Context to PubTator Entities and Relations | pubtator_context |
| Count PubTator Entity Co-occurrence from Sentence Context | pubtator_cooccurrence |
| Build a PubTator Relation Network with Evidence | pubtator_network |
| Search 'PubMed' Records | search_pubmed |